Missing vcf output

[Ida Bonde]

Hi

I am trying to use McCortex to find variant between two strains of yeast.
I have tried running it both with a reference and without using make-pipeline.pl and then make, but I don't get any output in the vcfs dir.

What I have done is:
With reference:
make-pipeline.pl -r ref.fa '31,41,51,61,71' output_dir V1vsV4_colour_list.tsv > my_job_script.mk
make -f my_job_script.mk CTXDIR=<mccortex_dir> MEM=40G NTHREADS=20

Without reference:
make-pipeline.pl '31,41,51,61,71' output_dir V1vsV4_colour_list.tsv > my_job_script.mk
make -f my_job_script.mk CTXDIR=<mccortex_dir> MEM=40G NTHREADS=20

The V1vsV4_colour_list.tsv file looks like:
V1      ../../trimmed/V1_S66_single.fastq.gz    ../../trimmed/V1_S66_R1_paired.fastq.gz:../../trimmed/V1_S66_R2_paired.fastq.gz .
V4      ../../trimmed/V4_S69_single.fastq.gz    ../../trimmed/V4_S69_R1_paired.fastq.gz:../../trimmed/V4_S69_R2_paired.fastq.gz .

When running with the reference I get output in the bubbles_links, graphs, links and ref directories for each of the kmers. Running without reference I get output in bubbles_links, bubbles_plain, graphs and links.
Looking at the log files I don't see any errors.
Do you have any idea where I could have gone wrong?

Best,
Ida

[Zamin Iqbal]

Hi there

This google group is for Cortex, not McCortex. Could you raise your question here please:

https://github.com/mcveanlab/mccortex/issues

cheers

Zam

[Ida Bonde]

Of cause sorry about that. The link to the mailing list on https://github.com/mcveanlab/mccortex goes here, so I though it might be a joined mailing list.

Best,

Ida

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